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@@ -37,9 +37,13 @@ sed -i 's/ //g' fasta/amplicon.fasta
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# CREATE OTU
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# DEDUPLICATION
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mkdir otu
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-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu
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-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu
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+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_otu.fasta
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+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_otu.fasta
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# REMOVING SINGLETON
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-soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu --minuniquesize 10
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-soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu --minuniquesize 10
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+soft/vsearch --derep_fulllength fasta/amplicon.fasta --output otu/fulllength_min10_otu.fasta --minuniquesize 10
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+soft/vsearch --derep_prefix fasta/amplicon.fasta --output otu/prefix_min10_otu.fasta --minuniquesize 10
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+
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+# REMOVING CHIMERAS
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+soft/vsearch --uchime_denovo otu/prefix_min10_otu.fasta --nonchimeras otu/prefix_min10_nochim_otu.fasta
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+soft/vsearch --uchime_denovo otu/fulllength_min10_otu.fasta --nonchimeras otu/fulllength_min10_nochim_otu.fasta
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nicolas-zimmermann